A possible risk of environmental exposure to HEV in Ibadan, Oyo State, Nigeria.

Hepatitis E virus (HEV) infection is both a major public health concern and emerging global health concern, with a documented incidence of 20 million, 3.4 million clinical cases, 70,000 deaths, and 3,000 stillbirths. The aetiologic agent, HEV is a primarily enterally transmitted hepatotropic virus. Fecal samples were collected from three selected pig farms across Ibadan, South-west Nigeria. Randomly picked samples were pooled per unit pen and fecal suspensions prepared were subjected to HEV Antigen (Ag) enzyme-linked immunosorbent assay. Molecular probing was done by Reverse Transcription and nested polymerase reaction (RT-nPCR) and deep sequencing. Sequencing was done paired-end for 300 cycles using the HiSeq system. Overall farm prevalence of 66.7% (2/3) and prevalence at individual level of 13.2% (9/68) were recorded. All nine samples positive for the ELISA screen were negative when subjected to RT-nPCR assays. Further, on deep sequencing, no HEV genomic fragment was found in the sample using de-novo assembly. Findings suggest possibly inapparent HEV in the pigs studied or a yet to be identified protein with HEV-Ag cross-reactivity ability on ELISA, thus constituting a possible risk of exposure to HEV infection in the population. Consequently, we recommend prompt intervention to unravel the mystery and break the chain of transmission.

Near-Complete Genome Sequence of an Enterovirus Species F Isolate Recovered from Sewage in Nigeria.

Here, we describe the near-complete genome of an enterovirus F (EV-F) isolate from Nigeria. The obtained sequence was 7,378 nucleotides (nt) long and encodes 2 open reading frames (ORFs), an upstream ORF (uORF; 56 amino acids [aa]) and a polyprotein ORF (ppORF; 2,167 aa). Both ORFs overlap but are in different reading frames, with the uORF in a +1 reading frame relative to the ppORF.

Genome Sequences of Novel Members of Previously Described DNA and RNA Virus Families, Isolated from Feces of a Drill Monkey in Nigeria.

The genomes of seven novel members of previously described DNA and RNA virus families are described here. These viruses were recovered using a viral metagenomic approach from the stool of a drill monkey (Mandrillus leucophaeus) housed in a sanctuary in Cross River State, Nigeria.

Reference Human Rotavirus A Genome Sequence from a Previously Vaccinated Child with Diarrhea in Nigeria.

In 2018, a 26-month-old girl, fully vaccinated with Rotarix in 2016, presented with fever, diarrhea, and vomiting. A rapid test showed that her feces contained rotavirus A (RVA). VP7 reverse transcription-PCR (RT-PCR) and Illumina sequencing showed that a G1P[8] strain with a Wa-like genotype constellation was the etiologic agent. This is the first near-complete RVA genome sequence from Nigeria.

Isolation and Genomic Characterization of Echovirus 11 from faeces of a Non-Human Primate in Nigeria.

We recently investigated the presence of enteroviruses (EVs) in non-human primates (NHPs) in Northern Nigeria and documented the presence of EV-A76 of South-East Asian ancestry in an NHP. In this study, we go further to ask if we could also find EVs in NHPs indigenous to the forested South-south Nigeria. Fresh faecal samples were collected from the floor of 10 cages housing NHPs in Cross River Nigeria, re-suspended in PBS and subjected to RNA extraction, cDNA synthesis, PanEnt 5'-UTR and PanEnt VP1 PCR assays. None of the samples was positive for the PanEnt VP1 assay, but one sample was positive for PanEnt 5'-UTR PCR. This sample was subsequently inoculated into RD cell line, produced CPE and the isolate analysed by PCR assays, next-generation whole genome sequencing and passage in four different cell lines showing replication in two of them. Analysis of the complete genome of the isolate identified it as an Echovirus 11 (E11) and revealed a recombinant genomic structure. Phylogenetic analysis showed that the E11 NHP strain was related to human clinical isolates suggesting a zoonotic behaviour. We describe the first isolation and complete genome characterization of an E11 obtained from an NHP in Nigeria having zoonotic potential.

Genomic Characterization of a Coxsackievirus A20 Strain Recovered from a Child with Acute Flaccid Paralysis in Nigeria.

In light of recurrent outbreaks of circulating vaccine-derived poliovirus 2 (cVDPV2) in Nigeria, we describe the genome sequence of a coxsackievirus A20 strain (CVA20). The nonstructural region (NSR) of this CVA20 genome showed that the enigmatic NSRs in recombinant cVDPV2s (GenBank accession numbers JX275140 and KX162716) found in Nigeria were from indigenous enterovirus species Cs (EV-Cs).

Genome Sequences of Two Dual-Serotype-Specific Echovirus 20 Strains from Nigeria.

Here, we describe nearly complete genome sequences (7,361 nucleotides [nt] and 6,893 nt) of two echovirus 20 (E20) isolates from Nigeria that were simultaneously typed as CVB and E20 (dual serotype) by neutralization assay. Both include two overlapping open reading frames (ORFs) of 67 and 2,183 amino acids that encoded a recently described gut infection-facilitating protein and the classic enterovirus proteins, respectively.

Hepatitis C virus seropositivity and the risk factors for transmission among blood donors in some selected centers in Lagos State, Southwest Nigeria.

Introduction: Hepatitis C virus (HCV) infects about 0.5% to 2.3% of the world population with most of the cases occurring in developing countries. It is primarily transmitted through transfusion of blood and blood products. There exists dearth of information on burden and circulation of HCV and their attendant health challenges in Nigeria. This study was therefore designed to determine the seroprevalence rate and risk of HCV transmission among blood donors in Lagos State Nigeria. Methodology: Blood samples were collected between January 2002 and December 2006 from 3,002 consenting (Male = 2,922; Female = 80; Age range = 18-63; Median age = 32 years) donors in five selected public hospitals' blood donation centers between 2002 and 2006. Sera was tested for anti-HCV by ELISA technique. Demographic and other relevant information were obtained by a semi-structured questionnaire to assess risk factors for HCV transmission. Results: This study found an overall rate of 3.1% for anti-HCV among the blood donors sampled. Highest rate of 6.0% for HCV was found among participants age ranged ≥50 years and lowest in the age group 40-49 years. Prevalence of HCV was higher in female (6.3%) than in male (3.0%) and was 0.21 times less risky in female compared to their male counterparts (OR = 1.29, 95%CI 0.11-1.31). By location, MSCH had the highest HCV rate (3.9%) and lowest (2.1%) in GHOA. Sharing of sharps for tattoo/tribal markings had a statistical association (p = .0379) with HCV infection. However, no significant difference was found by gender (CI = 0.99-2.01; p = .1002), age (CI = 0.79-1.55; p = .1001) and location (p = .5326). Conclusion: The relatively high prevalence of HCV infection detected and the risk of transmission among blood donors in this study are of public health importance. Hence, the institution of appropriate measures to stem down the trend of HCV circulation among this population in Nigeria is therefore advocated.

Genomic Characterization of an Echovirus 7 Isolate of Southeast Asian Ancestry Recovered from a Child in Nigeria with Acute Flaccid Paralysis.

Here, we describe the genome of an echovirus 7 (E7) isolate of Southeast Asian ancestry recovered from a child in Nigeria with acute flaccid paralysis (AFP). The genome has 7,295 nucleotides (nt) and an open reading frame (ORF) with 2,195 amino acids.

Draft Genome Sequence of a Bovine Enterovirus Isolate Recovered from Sewage in Nigeria.

We describe the draft genome of a bovine enterovirus (EV) isolate recovered from sewage in Nigeria. This isolate replicates on both RD and L20B cell lines but is negative for all EV screens in use by the Global Poliovirus Eradication Initiative (GPEI). It contains 7,368 nucleotides (nt) with 50.2% G+C content and an open reading frame (ORF) with 6,525 nt (2,174 amino acids).

Reference Echovirus 7 and 19 Genomes from Nigeria.

We describe the genomes of two echovirus isolates from Nigeria as reference enterovirus species B genomes for the region. These echovirus 7 and 19 genomes have 7,411 nucleotides (nt) and 7,426 nt and were recovered from sewage-contaminated water (in 2010) and an acute flaccid paralysis case (in 2014), respectively.

Draft Genome Sequence of Mycoplasma arginini Strain NGR_2017.

We present the draft genome of Mycoplasma arginini strain NGR_2017. This strain was recovered in Nigeria from cell culture in 2017. The assembly contains 620,555 bp in 12 contigs. It contains 561 coding sequences, 34 RNAs (29 tRNAs, 4 rRNAs, and 1 transfer-messenger RNA [tmRNA]), and a >26-kb integrative and conjugative element.

Patterns of serologic markers of hepatitis B virus infection and the risk of transmission among pregnant women in southwestern Nigeria.

Hepatitis B virus (HBV) infection is a major health concern in developing countries that has a high morbidity and mortality rate. Vertical transmission of HBV from mother to child has been identified as a major factor leading to chronicity with attendant liver conditions, especially in poor socioeconomic settings. This study aims to evaluate the prevalence of serological HBV markers among pregnant women in Ibadan southwestern Nigeria and to determine the implications for perinatal HBV transmission. This study revealed the presence of varied HBV serological patterns of infection or immunity among pregnant women in Ibadan, Nigeria, and thus the risk of mother to child transmission.

Non-polio enteroviruses in faeces of children diagnosed with acute flaccid paralysis in Nigeria.

BACKGROUND: The need to investigate the contribution of non-polio enteroviruses to acute flaccid paralysis (AFP) cannot be over emphasized as we move towards a poliovirus free world. Hence, we aim to identify non-polio enteroviruses recovered from the faeces of children diagnosed with AFP in Nigeria. METHODS: Ninety-six isolates, (95 unidentified and one previously confirmed Sabin poliovirus 3) recovered on RD cell culture from the stool of children <15 years old diagnosed with AFP in 2014 were analyzed. All isolates were subjected to RNA extraction, cDNA synthesis and three different PCR reactions (one panenterovirus 5'-UTR and two different VP1 amplification assays). VP1 amplicons were then sequenced and isolates identified. RESULTS: 92.71% (89/96) of the isolates were detected by at least one of the three assays as an enterovirus. Precisely, 79.17% (76/96), 6.25% (6/96), 7.30% (7/96) and 7.30% (7/96) of the isolates were positive for both, positive and negative, negative and positive, as well as negative for both the 5'-UTR and VP1 assays, respectively. In this study, sixty-nine (69) of the 83 VP1 amplicons sequenced were identified as 27 different enterovirus types. The most commonly detected were CV-B3 (10 isolates) and EV-B75 (5 isolates). Specifically, one, twenty-four and two of the enterovirus types identified in this study belong to EV-A, EV-B and EV-C respectively. CONCLUSIONS: This study reports the circulating strains of 27 non-polio enterovirus types in Nigerian children with AFP in 2014 and Nigerian strains of CV-B2, CV-B4, E17, EV-B80, EV-B73, EV-B97, EV-B93, EV-C99 and EV-A120 were reported for the first time. Furthermore, it shows that being positive for the 5'-UTR assay should not be the basis for subjecting isolates to the VP1 assays.

Seroprevalence of hepatitis B and delta viruses among HIV-infected population attending anti-retroviral clinic in selected health facilities in Abuja, Nigeria.

INTRODUCTION: Triple infection with human immunodeficiency virus (HIV), hepatitis B virus (HBV), and hepatitis D virus (HDV) is rare. There is limited data on the seroprevalence of HIV/HBV/HDV tri-infection especially in Nigeria. The aim of this study was to determine the seroprevalences of HBsAg and HDV among HIV-infected individuals attending anti-retroviral (ARV) clinics in Abuja, Nigeria. METHODS: In this cohort study, blood samples were collected from 1102 (male = 450; female = 652), with age range <20 to ≥51 years (mean age = 34.0; SD = 11.5), consenting HIV-infected population attending ARV clinics at selected health facilities in Abuja, Nigeria, between April and October 2016. A well-structured questionnaire was used to capture demographic information from the respondents. Enzyme-linked immunosorbent assay (ELISA) was used to determine the seroprevalence of hepatitis B surface antigen and anti-HDV. The result was interpreted according to manufacturer's instruction. Statistical data were analyzed using SPSS software version 21, and chi-square (χ2) test was used to determine association with P < 0.05 considered significant. RESULTS: Overall seroprevalences of 10.3%, 7.1%, and 0.7% for HBV, HBV/HDV, and HIV/HBV/HDV, respectively, were found among the study population. The infection rate (13.3%) peaked at age range of 31-40 years for HBV (P = 0.002), 50% at <20 years for HBV/HDV (P = 0.049), and 1.5% at 31-40 years for HIV/HBV/HDV (P = 0.202). By gender, the rate was higher in males (10.9%, 10.2%, 1.1%) than females (9.8%, 4.9%, 0.5%) for HBV, HBV/HDV, and HIV/HBV/HDV infections, respectively. However, there was no significant association between infection rate and gender. CONCLUSION: This study has established that HBV and HDV prevalence is still high in the population studied and that the rate of triple infection is low. We advocate for more robust control measures for HBV which should be extended to HDV in HIV population through screening and vaccination.

Preponderance of enterovirus C in RD-L20B-cell-culture-negative stool samples from children diagnosed with acute flaccid paralysis in Nigeria.

Recently, a reverse transcriptase semi-nested polymerase chain reaction (RT-snPCR) assay was recommended by the WHO for direct detection of enteroviruses in clinical specimens. In this study, we use this assay and a modification thereof to screen acute flaccid paralysis (AFP) samples that had previously tested negative for enteroviruses by the RD-L20B algorithm. Thirty paired stool suspensions collected in 2015 as part of the national AFP surveillance program in different states of Nigeria were analyzed in this study. The samples had previously tested negative for enteroviruses in the polio laboratory in accordance with the WHO-recommended RD-L20B-cell-culture-based algorithm. Two samples that had previously been found to contain enteroviruses were included as positive controls. All samples were subjected to RNA extraction, the RT-snPCR assay and a modified version of the RT-snPCR. All amplicons were sequenced, and enteroviruses were identified using the enterovirus genotyping tool and phylogenetic analysis. Amplicons were recovered from the two controls and 50% (15/30) of the samples screened. Fourteen were successfully typed, of which, 7.1% (1/14), 21.4% (3/14), 64.3% (9/14) and 7.1% (1/14) were enterovirus (EV) -A, EV-B, EV-C and a mixture of EV-B and C (EV-C99 and E25), respectively. The two controls were identified as EV-C99 and coxsackievirus (CV) -A1, both of which belong to the species Enterovirus C. In one sample, poliovirus serotype 2 was detected and found to have the VP1 ILE143 variation and was therefore identified as a vaccine strain. The results of this study showed that significant proportion of enterovirus infections (including some with Sabin PV2) are being missed by the RD-L20B-cell-culture-based algorithm, thus highlighting the value of the RT-snPCR assay and its modifications. The circulation and preponderance of EV-C in Nigeria was also confirmed.

Acute Hepatitis E Virus Infection in Two Geographical Regions of Nigeria.

Hepatitis E virus (HEV) remains a major public health concern in resource limited regions of the world. Yet data reporting is suboptimal and surveillance system is inadequate. In Nigeria, there is dearth of information on prevalence of acute HEV infection. This study was therefore designed to describe acute HEV infection among antenatal clinic attendees and community dwellers from two geographical regions in Nigeria. Seven hundred and fifty plasma samples were tested for HEV IgM by Enzyme Linked Immunosorbent Assay (ELISA) technique. The tested samples were randomly selected from a pool of 1,115 blood specimens previously collected for viral hepatitis studies among selected populations (pregnant women, 272; Oyo community dwellers, 438; Anambra community dwellers, 405) between September 2012 and August 2013. One (0.4%) pregnant woman in her 3rd trimester had detectable HEV IgM, while community dwellers from the two study locations had zero prevalence rates of HEV IgM. Detection of HEV IgM in a pregnant woman, especially in her 3rd trimester, is of clinical and epidemiological significance. The need therefore exists for establishment of a robust HEV surveillance system in Nigeria and especially amidst the pregnant population in a bid to improve maternal and child health.

Comparison of Algorithms for the Detection of Enteroviruses in Stool Specimens from Children Diagnosed with Acute Flaccid Paralysis.

This study was designed to compare both the cell culture dependent and independent enterovirus detection algorithms recommended by the WHO and assess how either might impact our perception of the diversity of enterovirus types present in a sample. Sixteen paired samples (16 isolates from RD cell culture and their corresponding stool suspension, i.e., 32 samples) from AFP cases in Nigeria were analyzed in this study. All the samples were subjected to RNA extraction, cDNA synthesis, the WHO recommended RT-snPCR, and its modification. Amplicons were sequenced and strains identified. Enterovirus diversity was the same between the isolates and fecal suspension for the control and five of the samples. It was, however, different for the remaining 10 (62.5%) samples. Nine (CV-B4, E6, E7, E13, E14, E19, E29, EV-B75, and EV-B77) and five (CV-A1, CV-A11, CV-A13, EV-C99, and PV2) EV-B and EV-C types, respectively, were detected. Particularly, E19 and EV-B75 were only recovered from the isolates while E14, EV-B77, CV-A11, and CV-A13 were only recovered from fecal suspension. Both the cell culture dependent and independent protocols bias our perception of the diversity of enterovirus types present in a sample. Hence, effort should be directed at harmonizing both for increased sensitivity.

High rate of unrecognized dengue virus infection in parts of the rainforest region of Nigeria.

Outbreaks and sporadic dengue virus infections continue to occur in Africa. Several reports of dengue among travellers returning from some African countries to Europe and North America have raised concerns about the epidemiological situation in Africa. We investigated recent dengue infections in febrile patients during the rainy season in various urban centres in the rainforest region of Nigeria, West Africa. This cross-sectional study was conducted for 8 months in 2014 with study participants from Adeoyo Hospital Yemetu - Ibadan, Nigeria. Plasma were collected from 274 febrile patients residing in 11 Local Government Areas of Oyo State. IgM antibodies were determined using semi-quantitative sandwich ELISA. Data was analyzed using Chi - Square and Fisher's exact test with SPSS 16.0. An overall prevalence of 23.4% dengue virus infection was found among study participants. Highest monthly prevalence of 40% was in April and August. The monthly distribution pattern of dengue virus infection indicates efficient virus transmission. Routine diagnosis will enhance dengue virus surveillance and improve patient care in West Africa.

Molecular detection of measles virus from children during a sporadic outbreak in two semi-urban areas in Nigeria.

BACKGROUND: According to the World Health Organization (WHO), African region accounts for 36% of deaths caused by measles worldwide. Nigeria has, over the years, recorded the highest average annual measles incidence per 100,000 populations in Africa. Measles epidemics have consistently been reported in northern Nigeria, but not in the South; reports of reduced protective haemagglutination inhibition antibody titers among children in Ibadan, southern Nigeria was made. Investigation of the viral agent responsible for the disease outbreak among children presenting with rash in two semi urban areas in southern Nigeria was carried out to confirm the etiology of the disease. METHODOLOGY: Twenty six throat swabs (TS), and nineteen urine samples were collected from twenty six children residing in Onireke and Sabo areas of Ibadan following the report of an outbreak of rashes among children. Active case finding with the support of community leaders was used to locate the affected children. Multiplex reverse transcriptase polymerase chain reaction (MRT-PCR), was used to identify the agent. RESULTS: 21 of the 26 children screened tested positive for measles virus, but none was positive for Rubella virus. There was significant association between measles infection, and households with higher number of persons. CONCLUSION: Mass measles vaccination that targets overcrowded, rural and inaccessible areas is needed to increase herd immunity. Public health enlightenment on the benefits of vaccination is encouraged.